<div dir="ltr">Elke<div><br></div><div>Can you send the files so I can check? Also what version are you using? And are you using the GUI?</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Nov 18, 2020 at 3:14 AM Schulz, Eike-Christian <<a href="mailto:eike.schulz@mpsd.mpg.de">eike.schulz@mpsd.mpg.de</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div lang="en-DE" style="overflow-wrap: break-word;">
<div class="gmail-m_-6762899975821242264WordSection1">
<p class="MsoNormal"><span lang="EN-US">Dear all, <u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">I am running phenix.ensemble_refinement on a covalent protein-ligand complex providing the same parameter-files used for phenix.refine. I also included the .def and .cif files generated by phenix.ligand_linking.
<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">However, in quite a few of the ensemble structures, the covalent link exceeds 5Å, which is obviously wrong. How can I obtain ensemble structures with reasonable covalent bond length?
<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span lang="DE">Best, <u></u><u></u></span></p>
<p class="MsoNormal"><span lang="DE"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="DE">Eike<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="DE"><u></u> <u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10pt;font-family:Tahoma,sans-serif;color:black">————————————————————————————<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10pt;color:rgb(102,102,102)">Dr. Eike C. Schulz </span><span lang="EN-US" style="font-size:10.5pt;color:black"><u></u><u></u></span></p>
<div>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.5pt;color:rgb(102,102,102)">Max Planck Institute for the Structure and Dynamics of Matter</span><span lang="EN-US" style="font-size:9.5pt;color:black"><u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.5pt;color:rgb(102,102,102)">Luruper Chaussee 149 | 22761 Hamburg | Germany</span><span lang="EN-US" style="font-size:9.5pt;color:black"><u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.5pt;color:rgb(102,102,102)">Building 99 (CFEL) | Office O2.101</span><span lang="EN-US" style="font-size:9.5pt;color:black"><u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.5pt;color:rgb(102,102,102)">Phone </span><span lang="EN-US" style="font-size:9.5pt;color:black"><a href="tel:%2B49%20%280%2940%208998-6264" target="_blank"><span style="color:rgb(17,85,204)">+49
(0)40 8998-6264</span></a></span><span lang="EN-US" style="font-size:9.5pt;color:rgb(102,102,102)"> | Fax </span><span lang="EN-US" style="font-size:9.5pt;color:black"><a href="tel:%2B49%20%280%2940%208994-6264" target="_blank"><span style="color:rgb(17,85,204)">+49
(0)40 8994-6264</span></a> | </span><span lang="EN-US" style="font-size:9.5pt;color:rgb(102,102,102)">Website </span><span lang="EN-US" style="font-size:9.5pt;color:black"><a href="http://www.mpsd.mpg.de/" target="_blank"><span style="color:rgb(17,85,204)">www.mpsd.mpg.de</span></a><u></u><u></u></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;color:black"> <u></u><u></u></span></p>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
</div>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote></div>